Task 38584209

Stderr output

<core_client_version>8.2.4</core_client_version>
<![CDATA[
<message>
The operating system cannot run (null).
 (0xc3) - exit code 195 (0xc3)</message>
<stderr_txt>
17:05:43 (11100): wrapper (7.9.26016): starting
17:05:43 (11100): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A09_A37_0.pdb
QB_A09_A37_0.xml
QB_A09_A37_equil.pdb
QB_A09_A37.inpcrd
QB_A09_A37_input.yaml
QB_A09_A37_mdlambda.pdb
QB_A09_A37_min.pdb
QB_A09_A37_npt.pdb
QB_A09_A37_out_merged_nowater.pdb
QB_A09_A37.pdb
QB_A09_A37.prmtop
QB_A09_A37_sys.xml
QB_A09_A37_therm.pdb
run.bat
run.sh
17:05:44 (11100): Library/usr/bin/tar.exe exited; CPU time 0.000000
17:05:44 (11100): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
  WARNING: The script pyaml.exe is installed in 'C:\ProgramData\BOINC\slots\0\Scripts' which is not on PATH.
  Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
  WARNING: The scripts abfe_production.exe, abfe_structprep.exe, make_atm_system_from_amber.exe, make_atm_system_from_pdb.exe, make_atm_system_from_rcpt_lig.exe, rbfe_production.exe and rbfe_structprep.exe are installed in 'C:\ProgramData\BOINC\slots\0\Scripts' which is not on PATH.
  Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {3835425} normal block at 0x000002286618D680, 8 bytes long.
 Data: <  }f(   > 00 00 7D 66 28 02 00 00 
..\lib\diagnostics_win.cpp(417) : {3833960} normal block at 0x0000022868054930, 1080 bytes long.
 Data: < L              > CC 4C 00 00 CD CD CD CD 14 03 00 00 00 00 00 00 
..\zip\boinc_zip.cpp(122) : {312} normal block at 0x0000022866181910, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
Object dump complete.
18:11:51 (21576): wrapper (7.9.26016): starting
18:11:51 (21576): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file C:\ProgramData\BOINC\slots\0\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1770} normal block at 0x0000021C7C8B5520, 8 bytes long.
 Data: <   |    > 00 00 86 7C 1C 02 00 00 
..\lib\diagnostics_win.cpp(417) : {305} normal block at 0x0000021C7C8B6450, 1080 bytes long.
 Data: < S              > 18 53 00 00 CD CD CD CD B0 00 00 00 00 00 00 00 
Object dump complete.
18:53:10 (14224): wrapper (7.9.26016): starting
18:53:10 (14224): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file C:\ProgramData\BOINC\slots\0\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1770} normal block at 0x0000020257E45F20, 8 bytes long.
 Data: <   W    > 00 00 DA 57 02 02 00 00 
..\lib\diagnostics_win.cpp(417) : {305} normal block at 0x0000020257E46450, 1080 bytes long.
 Data: <\T              > 5C 54 00 00 CD CD CD CD B0 01 00 00 00 00 00 00 
Object dump complete.
21:04:10 (15708): wrapper (7.9.26016): starting
21:04:10 (15708): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file C:\ProgramData\BOINC\slots\0\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1770} normal block at 0x000002BC114450C0, 8 bytes long.
 Data: <  <     > 00 00 3C 11 BC 02 00 00 
..\lib\diagnostics_win.cpp(417) : {305} normal block at 0x000002BC114463B0, 1080 bytes long.
 Data: <                > EC 17 00 00 CD CD CD CD 8C 01 00 00 00 00 00 00 
Object dump complete.
21:50:21 (8676): wrapper (7.9.26016): starting
21:50:21 (8676): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file C:\ProgramData\BOINC\slots\0\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1770} normal block at 0x000002D82FD06440, 8 bytes long.
 Data: <   /    > 00 00 CB 2F D8 02 00 00 
..\lib\diagnostics_win.cpp(417) : {305} normal block at 0x000002D82FD07090, 1080 bytes long.
 Data: <$!              > 24 21 00 00 CD CD CD CD 8C 01 00 00 00 00 00 00 
Object dump complete.
23:57:13 (7844): wrapper (7.9.26016): starting
23:57:13 (7844): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file C:\ProgramData\BOINC\slots\0\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1770} normal block at 0x00000204647C5070, 8 bytes long.
 Data: <  4f    > 00 00 34 66 04 02 00 00 
..\lib\diagnostics_win.cpp(417) : {305} normal block at 0x00000204647C6450, 1080 bytes long.
 Data: < Z              > C8 5A 00 00 CD CD CD CD A8 01 00 00 00 00 00 00 
Object dump complete.
00:49:03 (10932): wrapper (7.9.26016): starting
00:49:03 (10932): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file C:\ProgramData\BOINC\slots\0\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Traceback (most recent call last):
  File "<frozen runpy>", line 198, in _run_module_as_main
  File "<frozen runpy>", line 88, in _run_code
  File "C:\ProgramData\BOINC\slots\0\Scripts\rbfe_production.exe\__main__.py", line 7, in <module>
  File "C:\ProgramData\BOINC\slots\0\Lib\site-packages\atom_openmm\rbfe_production.py", line 33, in rbfe_production
    rx.scheduleJobs()
  File "C:\ProgramData\BOINC\slots\0\Lib\site-packages\atom_openmm\async_re.py", line 321, in scheduleJobs
    self.transport.ProcessJobQueue(min_time,cycle_time)
  File "C:\ProgramData\BOINC\slots\0\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 186, in ProcessJobQueue
    self.isDone(repl,0)
  File "C:\ProgramData\BOINC\slots\0\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 287, in isDone
    retcode = self._update_replica(job)
              ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\0\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 212, in _update_replica
    pot = job['openmm_worker'].get_energy()
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\0\Lib\site-packages\atom_openmm\ommworker.py", line 451, in get_energy
    return self._worker_getenergy()
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\0\Lib\site-packages\atom_openmm\ommworker.py", line 400, in _worker_getenergy
    state = self.simulation.context.getState(getEnergy = True)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\0\Lib\site-packages\openmm\openmm.py", line 5022, in getState
    state = _openmm.Context_getState(self, types, enforcePeriodicBox, groups_mask)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
openmm.OpenMMException: Particle coordinate is NaN.  For more information, see https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#nan
01:17:24 (10932): C:/Windows/system32/cmd.exe exited; CPU time 1759.343750
01:17:24 (10932): app exit status: 0x16
01:17:24 (10932): called boinc_finish(195)
0 bytes in 0 Free Blocks.
256 bytes in 6 Normal Blocks.
1144 bytes in 1 CRT Blocks.
0 bytes in 0 Ignore Blocks.
0 bytes in 0 Client Blocks.
Largest number used: 0 bytes.
Total allocations: 26617640 bytes.
Dumping objects ->
{1858} normal block at 0x00000167A86E49B0, 48 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1847} normal block at 0x00000167A86E48D0, 48 bytes long.
 Data: <HOME=C:\ProgramD> 48 4F 4D 45 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1836} normal block at 0x00000167A86E4A20, 48 bytes long.
 Data: <TMP=C:\ProgramDa> 54 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 61 
{1825} normal block at 0x00000167A86E4D30, 48 bytes long.
 Data: <TEMP=C:\ProgramD> 54 45 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1814} normal block at 0x00000167A86E4CC0, 48 bytes long.
 Data: <TMPDIR=C:\Progra> 54 4D 50 44 49 52 3D 43 3A 5C 50 72 6F 67 72 61 
{1783} normal block at 0x00000167A86CF580, 64 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
..\api\boinc_api.cpp(309) : {1770} normal block at 0x00000167A86E5610, 8 bytes long.
 Data: <    g   > 00 00 D5 A8 67 01 00 00 
{306} normal block at 0x00000167A86E57F0, 8 bytes long.
 Data: <Pdn g   > 50 64 6E A8 67 01 00 00 
{297} normal block at 0x00000167A86D1B60, 80 bytes long.
 Data: </c call Scripts\> 2F 63 20 63 61 6C 6C 20 53 63 72 69 70 74 73 5C 
{296} normal block at 0x00000167A86E53E0, 16 bytes long.
 Data: <Xcn g           > 58 63 6E A8 67 01 00 00 00 00 00 00 00 00 00 00 
{295} normal block at 0x00000167A86E5C00, 16 bytes long.
 Data: <0cn g           > 30 63 6E A8 67 01 00 00 00 00 00 00 00 00 00 00 
{294} normal block at 0x00000167A86DFDE0, 32 bytes long.
 Data: <r0/checkpoint.xm> 72 30 2F 63 68 65 63 6B 70 6F 69 6E 74 2E 78 6D 
{293} normal block at 0x00000167A86E5480, 16 bytes long.
 Data: < cn g           > 08 63 6E A8 67 01 00 00 00 00 00 00 00 00 00 00 
{292} normal block at 0x00000167A86E5ED0, 16 bytes long.
 Data: < bn g           > E0 62 6E A8 67 01 00 00 00 00 00 00 00 00 00 00 
{291} normal block at 0x00000167A86E5340, 16 bytes long.
 Data: < bn g           > B8 62 6E A8 67 01 00 00 00 00 00 00 00 00 00 00 
{290} normal block at 0x00000167A86E56B0, 16 bytes long.
 Data: < bn g           > 90 62 6E A8 67 01 00 00 00 00 00 00 00 00 00 00 
{289} normal block at 0x00000167A86E4EF0, 48 bytes long.
 Data: <ComSpec=C:\Windo> 43 6F 6D 53 70 65 63 3D 43 3A 5C 57 69 6E 64 6F 
{288} normal block at 0x00000167A86E5A70, 16 bytes long.
 Data: <  m g           > 18 0A 6D A8 67 01 00 00 00 00 00 00 00 00 00 00 
{287} normal block at 0x00000167A86E0680, 32 bytes long.
 Data: <SystemRoot=C:\Wi> 53 79 73 74 65 6D 52 6F 6F 74 3D 43 3A 5C 57 69 
{286} normal block at 0x00000167A86E5A20, 16 bytes long.
 Data: <  m g           > F0 09 6D A8 67 01 00 00 00 00 00 00 00 00 00 00 
{284} normal block at 0x00000167A86E55C0, 16 bytes long.
 Data: <  m g           > C8 09 6D A8 67 01 00 00 00 00 00 00 00 00 00 00 
{283} normal block at 0x00000167A86E51B0, 16 bytes long.
 Data: <  m g           > A0 09 6D A8 67 01 00 00 00 00 00 00 00 00 00 00 
{282} normal block at 0x00000167A86E5E30, 16 bytes long.
 Data: <x m g           > 78 09 6D A8 67 01 00 00 00 00 00 00 00 00 00 00 
{281} normal block at 0x00000167A86E5520, 16 bytes long.
 Data: <P m g           > 50 09 6D A8 67 01 00 00 00 00 00 00 00 00 00 00 
{280} normal block at 0x00000167A86E5E80, 16 bytes long.
 Data: <( m g           > 28 09 6D A8 67 01 00 00 00 00 00 00 00 00 00 00 
{279} normal block at 0x00000167A86DF8A0, 32 bytes long.
 Data: <CUDA_DEVICE=0 PU> 43 55 44 41 5F 44 45 56 49 43 45 3D 30 00 50 55 
{278} normal block at 0x00000167A86E5160, 16 bytes long.
 Data: <  m g           > 00 09 6D A8 67 01 00 00 00 00 00 00 00 00 00 00 
{277} normal block at 0x00000167A86D0900, 320 bytes long.
 Data: <`Qn g     m g   > 60 51 6E A8 67 01 00 00 A0 F8 6D A8 67 01 00 00 
{276} normal block at 0x00000167A86E5570, 16 bytes long.
 Data: <pbn g           > 70 62 6E A8 67 01 00 00 00 00 00 00 00 00 00 00 
{275} normal block at 0x00000167A86E52F0, 16 bytes long.
 Data: <Hbn g           > 48 62 6E A8 67 01 00 00 00 00 00 00 00 00 00 00 
{274} normal block at 0x00000167A86E0500, 32 bytes long.
 Data: <C:/Windows/syste> 43 3A 2F 57 69 6E 64 6F 77 73 2F 73 79 73 74 65 
{273} normal block at 0x00000167A86E5070, 16 bytes long.
 Data: < bn g           > 20 62 6E A8 67 01 00 00 00 00 00 00 00 00 00 00 
{272} normal block at 0x00000167A86DFA80, 32 bytes long.
 Data: <xjvf input.tar.b> 78 6A 76 66 20 69 6E 70 75 74 2E 74 61 72 2E 62 
{271} normal block at 0x00000167A86E5DE0, 16 bytes long.
 Data: <han g           > 68 61 6E A8 67 01 00 00 00 00 00 00 00 00 00 00 
{270} normal block at 0x00000167A86E5110, 16 bytes long.
 Data: <@an g           > 40 61 6E A8 67 01 00 00 00 00 00 00 00 00 00 00 
{269} normal block at 0x00000167A86E5840, 16 bytes long.
 Data: < an g           > 18 61 6E A8 67 01 00 00 00 00 00 00 00 00 00 00 
{268} normal block at 0x00000167A86E5430, 16 bytes long.
 Data: < `n g           > F0 60 6E A8 67 01 00 00 00 00 00 00 00 00 00 00 
{267} normal block at 0x00000167A86E59D0, 16 bytes long.
 Data: < `n g           > C8 60 6E A8 67 01 00 00 00 00 00 00 00 00 00 00 
{266} normal block at 0x00000167A86E5980, 16 bytes long.
 Data: < `n g           > A0 60 6E A8 67 01 00 00 00 00 00 00 00 00 00 00 
{264} normal block at 0x00000167A86E5B60, 16 bytes long.
 Data: <PLn g           > 50 4C 6E A8 67 01 00 00 00 00 00 00 00 00 00 00 
{263} normal block at 0x00000167A86E4C50, 40 bytes long.
 Data: <`[n g     l g   > 60 5B 6E A8 67 01 00 00 80 F5 6C A8 67 01 00 00 
{262} normal block at 0x00000167A86E5750, 16 bytes long.
 Data: < `n g           > 80 60 6E A8 67 01 00 00 00 00 00 00 00 00 00 00 
{261} normal block at 0x00000167A86E58E0, 16 bytes long.
 Data: <X`n g           > 58 60 6E A8 67 01 00 00 00 00 00 00 00 00 00 00 
{260} normal block at 0x00000167A86E0620, 32 bytes long.
 Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F 
{259} normal block at 0x00000167A86E5AC0, 16 bytes long.
 Data: <0`n g           > 30 60 6E A8 67 01 00 00 00 00 00 00 00 00 00 00 
{258} normal block at 0x00000167A86E6030, 992 bytes long.
 Data: < Zn g     n g   > C0 5A 6E A8 67 01 00 00 20 06 6E A8 67 01 00 00 
{94} normal block at 0x00000167A86E05C0, 32 bytes long.
 Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F 
{93} normal block at 0x00000167A86DE260, 16 bytes long.
 Data: <  l g           > 20 F1 6C A8 67 01 00 00 00 00 00 00 00 00 00 00 
{92} normal block at 0x00000167A86CF120, 40 bytes long.
 Data: <` m g     n g   > 60 E2 6D A8 67 01 00 00 C0 05 6E A8 67 01 00 00 
{71} normal block at 0x00000167A86DDA90, 16 bytes long.
 Data: <   B            > 80 EA 01 42 F6 7F 00 00 00 00 00 00 00 00 00 00 
{70} normal block at 0x00000167A86DE170, 16 bytes long.
 Data: <@  B            > 40 E9 01 42 F6 7F 00 00 00 00 00 00 00 00 00 00 
{69} normal block at 0x00000167A86DE030, 16 bytes long.
 Data: < W A            > F8 57 FE 41 F6 7F 00 00 00 00 00 00 00 00 00 00 
{68} normal block at 0x00000167A86DDFE0, 16 bytes long.
 Data: < W A            > D8 57 FE 41 F6 7F 00 00 00 00 00 00 00 00 00 00 
{67} normal block at 0x00000167A86DDF90, 16 bytes long.
 Data: <P  A            > 50 04 FE 41 F6 7F 00 00 00 00 00 00 00 00 00 00 
{66} normal block at 0x00000167A86DD540, 16 bytes long.
 Data: <0  A            > 30 04 FE 41 F6 7F 00 00 00 00 00 00 00 00 00 00 
{65} normal block at 0x00000167A86DDEF0, 16 bytes long.
 Data: <   A            > E0 02 FE 41 F6 7F 00 00 00 00 00 00 00 00 00 00 
{64} normal block at 0x00000167A86DE3A0, 16 bytes long.
 Data: <   A            > 10 04 FE 41 F6 7F 00 00 00 00 00 00 00 00 00 00 
{63} normal block at 0x00000167A86DE440, 16 bytes long.
 Data: <p  A            > 70 04 FE 41 F6 7F 00 00 00 00 00 00 00 00 00 00 
{62} normal block at 0x00000167A86DDAE0, 16 bytes long.
 Data: <   A            > 18 C0 FC 41 F6 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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